clusterVisualHclust-class {goCluster} | R Documentation

## Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.

### Description

This class can be used in order to visualize annotation terms that have been found as overrepresented in clusters identified with a hierarchical clustering. These annotation terms are displayed alongside the hierarchical clustering result.

### Details

The class provides a wrapper around the `prepareAxis`-function. Please read the corresponding documentation for further details.

### Slots

`prepared`:
  Object of class `"list"`, the number of vectors stored in this list corresponds to the number of annotations analyzed. Each vector contains the same number of items as there are nodes in the tree of the clustering (number of genes - 1). The order of appearence corresponds to the ordering of the dendrogram so that the sorted dendrogram and the annotation terms can be put alongside each other.

Additional slots are described in the documentation of the `clusterVisual-class` and `clusterModule-class`.

### Extends

Class `"clusterVisual"`, directly. Class `"clusterModule"`, by class `"clusterVisual"`.

### Methods

config
  `signature(object = "clusterVisualHclust")`: interactive setup of the class. There are no options that you can set on this class.
setup
  `signature(object = "clusterVisualHclust")`: returns the configuration of the object as a list. Since there are no options to this class, this is always an empty list.
setup<-
  `signature(object = "clusterVisualHclust")`: non-interactive setup of the class. Not necessary since this class has no options.
execute
  `signature(object = "clusterVisualHclust")`: prepares the selected annotation terms for the visualization.
reset
  `signature(object = "clusterVisualHclust")`: resets the results of this class so that the analysis can be run again.
display
  `signature(object = "clusterVisualHclust")`: generates the actual graphic for this object.
print
  `signature(x = "clusterVisualHclust")`: prints generic information about the object.

### Author(s)

Gunnar Wrobel, http://www.gunnarwrobel.de.

### See Also

`prepareAxis`, `goCluster-class`, `clusterModule-class`, `clusterVisual-class`

### Examples

    set.seed(1000)

    data(benomylsetupsmall)

    benomylsetupsmall$classalgo <- "clusterAlgorithmHclust"
    benomylsetupsmall$algo$method   <- "complete"
    benomylsetupsmall$algo$distance <- "euclidean"

    benomylsetupsmall$classvisu <- "clusterVisualHclust"

    a <- new("goCluster")

    execute(a) <- benomylsetupsmall

    if(interactive()){
    ## This example can only be run in an interactive mode

    ## This plot shows only one labeled region since the
    ## loaded dataset has been reduced to only 100 genes.
    ## Try the same with the full dataset
    display(a, selection = 1)
    }

[Package goCluster version 1.0.3 Index]